scholarly journals Acinetobacter gandensis sp. nov. isolated from horse and cattle

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4007-4015 ◽  
Author(s):  
Annemieke Smet ◽  
Piet Cools ◽  
Lenka Krizova ◽  
Martina Maixnerova ◽  
Ondrej Sedo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Tof Ms

We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA–DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467T showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467T showed the highest similarities with ‘Acinetobacter bohemicus’ ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467T were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467T and UG 60716 showed a DNA–DNA relatedness of 84 % with each other and a DNA–DNA relatedness with A. schindleri LMG 19576T of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467T was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467T ( = ANC 4275T = LMG 27960T = DSM 28097T).

scholarly journals Frigoribacterium endophyticum sp. nov., an endophytic actinobacterium isolated from the root of Anabasis elatior (C. A. Mey.) Schischk

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1207-1212 ◽  
Author(s):  
Hong-Fei Wang ◽  
Yong-Guang Zhang ◽  
Ji-Yue Chen ◽  
Jian-Wei Guo ◽  
Li Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Endophytic Actinobacterium

A novel endophytic actinobacterium, designated EGI 6500707T, was isolated from the surface-sterilized root of a halophyte Anabasis elatior (C. A. Mey.) Schischk collected from Urumqi, Xinjiang province, north-west China, and characterized using a polyphasic approach. Cells were Gram-stain-positive, non-motile, short rods and produced white colonies. Growth occurred at 10–45 °C (optimum 25–30 °C), at pH 5–10 (optimum pH 8) and in presence of 0–4 % (w/v) NaCl (optimum 0–3 %). The predominant menaquinone was MK-9. The diagnostic phospholipids were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content of strain EGI 6500707T was 69.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain EGI 6500707T should be placed in the genus Frigoribacterium (family Microbacteriaceae , phylum Actinobacteria ), and that the novel strain exhibited the highest 16S rRNA gene sequence similarity to Frigoribacterium faeni JCM 11265T (99.1 %) and Frigoribacterium mesophilum MSL-08T (96.5 %). DNA–DNA relatedness between strain EGI 6500707T and F. faeni JCM 11265T was 47.2 %. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain EGI 6500707T represents a novel species of the genus Frigoribacterium , for which the name Frigoribacterium endophyticum sp. nov. is proposed. The type strain is EGI 6500707T ( = JCM 30093T = KCTC 29493T).

Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1776-1781 ◽  
Author(s):  
Jian Zhang ◽  
Zi-Ting Wang ◽  
Hui-Min Yu ◽  
Yuchao Ma
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A bacterial strain, designated D75T, was isolated from the rhizosphere soil of Catalpa speciosa. Phylogenetic analysis based on the complete 16S rRNA gene sequence revealed that strain D75T was a member of the genus Paenibacillus . High levels of 16S rRNA gene sequence similarity were found between strain D75T and Paenibacillus glycanilyticus DS-1T (99.2 %), Paenibacillus xinjiangensis B538T (97.5 %) and Paenibacillus castaneae Ch-32T (97.2 %). The chemotaxonomic properties of strain D75T were consistent with those of the genus Paenibacillus : the cell-wall peptidoglycan type was based on meso-diaminopimelic acid (A1γ), the predominant menaquinone was MK-7, and the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. However, levels of DNA–DNA relatedness between strain D75T and P. glycanilyticus NBRC 16618T, P. xinjiangensis DSM 16970T and P. castaneae DSM 19417T were 35, 20 and 18 %, respectively. On the basis of phenotypic and chemotaxonomic analyses, phylogenetic data and DNA–DNA relatedness values, strain D75T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus catalpae sp. nov. is proposed. The type strain is D75T ( = DSM 24714T = CGMCC 1.10784T).

scholarly journals Lysinibacillus varians sp. nov., an endospore-forming bacterium with a filament-to-rod cell cycle

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3644-3649 ◽  
Author(s):  
Chunjie Zhu ◽  
Guoping Sun ◽  
Xingjuan Chen ◽  
Jun Guo ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Single Cells ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Six Gram-stain-positive, motile, filamentous and/or rod-shaped, spherical spore-forming bacteria (strains GY32T, L31, F01, F03, F06 and F07) showing polybrominated diphenyl ether transformation were investigated to determine their taxonomic status. After spore germination, these organisms could grow more than one hundred microns long as intact single cells and then divide into rod cells and form endospores in 33 h. The cell-wall peptidoglycan of these strains was type A4α, the predominant menaquinone was MK-7 and the major fatty acids were iso-C16 : 0, iso-C15 : 0 and C16 : 1ω7C. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine were detected in the polar lipid profile. Analysis of the 16S rRNA gene sequences indicated that these strains should be placed in the genus Lysinibacillus and they were most closely related to Lysinibacillus sphaericus DSM 28T (99 % 16S rRNA gene sequence similarity). The gyrB sequence similarity and DNA–DNA relatedness between strain GY32T and L. sphaericus JCM 2502T were 81 % and 52 %, respectively. The G+C content of the genomic DNA of strain GY32T was 43.2 mol%. In addition, strain GY32T showed differences in nitrate reduction, starch and gelatin hydrolysis, carbon resource utilization and cell morphology. The phylogenetic distance from its closest relative measured by DNA–DNA relatedness and DNA G+C content, and its phenotypic properties demonstrated that strain GY32T represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus varians sp. nov. is proposed. The type strain is GY32T ( = NBRC 109424T = CGMCC 1.12212T = CCTCC M 2011307T).

Thalassolituus marinus sp. nov., a hydrocarbon-utilizing marine bacterium

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2234-2238 ◽  
Author(s):  
Ahyoung Choi ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Gram-negative strains, motile by a single polar flagellum, non-pigmented and with a curved rod-shaped morphology, designated IMCC1826T and IMCC1883, were isolated from a surface seawater sample from the Yellow Sea. The two strains shared 99.9 % 16S rRNA gene sequence similarity and showed 92 % DNA–DNA relatedness, suggesting that they belonged to the same genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates were related most closely to the type strain of Thalassolituus oleivorans with a sequence similarity of 96.4 % and formed a robust phyletic lineage with T. oleivorans . DNA–DNA relatedness between the two strains and T. oleivorans DSM 14913T was 8.7–11.6 %. A putative alkane hydroxylase (alkB) gene was detected in strain IMCC1826T by PCR, but the amino acid sequence of the gene was distantly related to that of the AlkB homologue of T. oleivorans DSM 14913T. As expected from the presence of the alkB gene, the new strains utilized n-tetradecane and n-hexadecane as a carbon source. The DNA G+C content was 54.6–56.0 mol% and the main isoprenoid quinone detected was Q-9. Polar lipids of strain IMCC1826T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and amino-group-containing lipids. On the basis of taxonomic data obtained in this study, strains IMCC1826T and IMCC1883 represent a novel species of the genus Thalassolituus , for which the name Thalassolituus marinus sp. nov. is proposed, with IMCC1826T ( = KCTC 23084T = NBRC 107590T) as the type strain.

scholarly journals Description of Kribbella italica sp. nov., isolated from a Roman catacomb

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 491-496 ◽  
Author(s):  
Gareth J. Everest ◽  
Sarah M. Curtis ◽  
Filomena De Leo ◽  
Clara Urzì ◽  
Paul R. Meyers
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinobacterium, strain BC637T, was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637T was most closely related to the type strains of Kribbella lupini and Kribbella endophytica . DNA–DNA hybridization experiments confirmed that strain BC637T is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718T (63 % DNA relatedness) and K. lupini LU14T (63 % DNA relatedness). Physiological comparisons showed that strain BC637T is phenotypically distinct from the type strains of K. endophytica and K. lupini . Thus, strain BC637T represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967T = NRRL B-59155T).

scholarly journals Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 856-859 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Song-Ih Han ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Xanthomonas Campestris ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two actinobacterial strains, JR-43T and JR-4, were isolated from bamboo (Sasa borealis) rhizosphere soil. The isolates produced grey aerial mycelium and a yellow soluble pigment on ISP 4. Microscopic observation revealed that strains JR-43T and JR-4 produced rectiflexibiles spore chains with spiny surfaces. Both isolates had antibacterial activity against plant-pathogenic bacteria, such as Xanthomonas campestris LMG 568T and Xanthomonas axonopodis pv. vesicatoria LMG 905. The isolates contained iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids and MK-9(H6) and MK-9(H8) as the major isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences of strains JR-43T and JR-4 showed that they grouped within Streptomyces cluster II and had highest sequence similarity to Streptomyces seoulensis NBRC 16668T and Streptomyces recifensis NBRC 12813T (both 98.2 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain JR-43T and S. seoulensis NBRC 16668T and S. recifensis NBRC 12813T ranged from 31.42 to 42.92 %. Based on DNA–DNA relatedness and morphological and phenotypic data, strains JR-43T and JR-4 could be distinguished from the type strains of phylogenetically related species. They are therefore considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces gramineus sp. nov. is proposed. The type strain is JR-43T ( = KACC 15079T  = NBRC 107863T). Strain JR-43 ( = KACC 15078  = NBRC 107864) is a reference strain.

scholarly journals Paracoccus panacisoli sp. nov., isolated from a forest soil cultivated with Vietnamese ginseng

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1491-1497 ◽  
Author(s):  
Ngoc-Lan Nguyen ◽  
Yeon-Ju Kim ◽  
Van-An Hoang ◽  
Bao-Tram Tran ◽  
Huong-Son Pham ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

A novel bacterial strain, designated DCY94T, was isolated from forest soil cultivated with ginseng in Vietnam. The strain was Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped and catalase- and oxidase-positive. 16S rRNA gene sequence analysis demonstrated that strain DCY94T was closely related to Paracoccus sphaerophysae Zy-3T (97.5 % 16S rRNA gene sequence similarity) and Paracoccus caeni MJ17T (96.9 %). The fatty acid profile of strain DCY94T contained a predominant amount of summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 88.4 %) and moderate to small quantities of C8 : 0 3-OH (1.0 %), C10 : 0 3-OH (2.8 %) and C18 : 0 (5.2 %). Phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and one unidentified glycolipid were major polar lipids; one unidentified aminolipid, one unidentified aminophospholipid, one unidentified phospholipid and four unidentified polar lipids were minor components. The polyamine pattern comprised the major compounds putrescine and spermidine and minor amounts of sym-homospermidine and spermine. The ubiquinone of the strain was Q-10 and the G+C content of its genomic DNA was 68.3 mol%. All these results support the placement of strain DCY94T within the genus Paracoccus . Levels of DNA–DNA relatedness between strain DCY94T and P. sphaerophysae HAMBI 3106T and P. caeni KCTC 22480T were 52 and 50 %, respectively. The results of phylogenetic analysis, phenotypic tests, chemotaxonomic characterization and DNA–DNA relatedness studies distinguished strain DCY94T from the closest recognized species of the genus Paracoccus , suggesting that this strain represents a novel species, for which the name Paracoccus panacisoli sp. nov. is proposed. The type strain is DCY94T ( = KCTC 42086T = JCM 30337T).

scholarly journals Microbacterium shaanxiense sp. nov., isolated from the nodule surface of soybean

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1437-1443 ◽  
Author(s):  
Shi Peng ◽  
Liu Dongying ◽  
Yang Bingxin ◽  
Li Mingjun ◽  
Wei Gehong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Physiological And Biochemical Characteristics

A Gram-stain-positive, non-motile, catalase- and oxidase-positive rod, designated CCNWSP60T, was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. 16S rRNA gene sequence analysis clearly showed that the isolate belonged to the genus Microbacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP60T was most closely related to Microbacterium murale DSM 22178T (98.8 % similarity), Microbacterium aerolatum DSM 14217T (98.3 %), Microbacterium ginsengiterrae DSM 24823T (98.0 %) and Microbacterium profundi DSM 22239T (97.8 %). However, the DNA–DNA relatedness values of strain CCNWSP60T to M. murale DSM 22178T, M. aerolatum DSM 14217T, M. ginsengiterrae DSM 24823T and M. profundi DSM 22239T were 48 %, 43 %, 28 % and 41 %, respectively. Growth of strain CCNWSP60T occurred at 4–40 °C and at pH 5.0–9.0. The NaCl range for growth was 0–4 % (w/v). The predominant menaquinone of strain CCNWSP60T was MK-13; MK-12 was also detected. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified glycolipid and one unidentified phospholipid. The diagnostic diamino acid of the peptidoglycan was ornithine. The acyl type of the peptidoglycan was glycolyl. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The DNA G+C content of the type strain was 67.4 mol%. As the physiological and biochemical characteristics as well as the DNA–DNA relatedness between strain CCNWSP60T and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species Microbacterium shaanxiense is proposed to accommodate it. The type strain is CCNWSP60T ( = DSM 28301T = ACCC 19329T = JCM 30164T).

scholarly journals Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 2944-2948 ◽  
Author(s):  
Collette Fitzgerald ◽  
Zheng chao Tu ◽  
Mary Patrick ◽  
Tracy Stiles ◽  
Andy J. Lawson ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Campylobacter Fetus ◽  
Phenotypic Tests ◽  
Tof Ms

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus -like strains from humans (n = 8) and reptiles (n = 5). The results of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and genomic data from sap analysis, 16S rRNA gene and hsp60 sequence comparison, pulsed-field gel electrophoresis, amplified fragment length polymorphism analysis, DNA–DNA hybridization and whole genome sequencing demonstrated that these strains are closely related to C. fetus but clearly differentiated from recognized subspecies of C. fetus . Therefore, this unique cluster of 13 strains represents a novel subspecies within the species C. fetus , for which the name Campylobacter fetus subsp. testudinum subsp. nov. is proposed, with strain 03-427T ( = ATCC BAA-2539T = LMG 27499T) as the type strain. Although this novel taxon could not be differentiated from C. fetus subsp. fetus and C. fetus subsp. venerealis using conventional phenotypic tests, MALDI-TOF MS revealed the presence of multiple phenotypic biomarkers which distinguish Campylobacter fetus subsp. testudinum subsp. nov. from recognized subspecies of C. fetus .

scholarly journals Lactobacillus nasuensis sp. nov., a lactic acid bacterium isolated from silage, and emended description of the genus Lactobacillus

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1140-1144 ◽  
Author(s):  
Yimin Cai ◽  
Huili Pang ◽  
Maki Kitahara ◽  
Moriya Ohkuma
Keyword(s):  
Lactic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two strains of lactic acid bacteria, designated SU 18T and SU 83, were isolated from silage prepared with Sudan grass [Sorghum sudanense (Piper) Stapf.]. The isolates were Gram-stain-positive, catalase-negative, facultatively anaerobic rods that did not produce gas from glucose. The isolates exhibited ≥93.5 % DNA–DNA relatedness to each other and shared the same phenotypic characteristics, which indicated that they belonged to a single species. The DNA G+C content was 58.5–59.2 mol%. On the basis of 16S rRNA gene sequence analysis, the isolates were placed in the genus Lactobacillus . Their closest phylogenetic neighbours were Lactobacillus manihotivorans JCM 12514T and Lactobacillus camelliae JCM 13995T (95.9 and 96.8 % 16S rRNA gene sequence similarity, respectively, with strain SU 18T). Ribotyping revealed that strain SU 18T was well separated from L. manihotivorans JCM 12514T and L. camelliae JCM 13995T. Strain SU 18T exhibited ≤23.7 % DNA–DNA relatedness with its closest phylogenetic neighbours. The isolates represent a novel species in the genus Lactobacillus , for which the name Lactobacillus nasuensis sp. nov. is proposed. The type strain is SU 18T ( = JCM 17158T  = CGMCC 1.10801T). The description of the genus Lactobacillus is also amended.

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